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- PDB-5lih: Structure of a peptide-substrate bound to PKCiota core kinase domain -
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Open data
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Basic information
Entry | Database: PDB / ID: 5lih | ||||||
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Title | Structure of a peptide-substrate bound to PKCiota core kinase domain | ||||||
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![]() | TRANSFERASE / aPKC / Polarity / Complex | ||||||
Function / homology | ![]() positive regulation of cellular glucuronidation / ethanol binding / TRAM-dependent toll-like receptor 4 signaling pathway / diacylglycerol-dependent, calcium-independent serine/threonine kinase activity / Golgi vesicle budding / PAR polarity complex / Tight junction interactions / establishment of apical/basal cell polarity / DAG and IP3 signaling / protein kinase C ...positive regulation of cellular glucuronidation / ethanol binding / TRAM-dependent toll-like receptor 4 signaling pathway / diacylglycerol-dependent, calcium-independent serine/threonine kinase activity / Golgi vesicle budding / PAR polarity complex / Tight junction interactions / establishment of apical/basal cell polarity / DAG and IP3 signaling / protein kinase C / positive regulation of lipid catabolic process / negative regulation of glial cell apoptotic process / eye photoreceptor cell development / negative regulation of sodium ion transmembrane transporter activity / mucus secretion / diacylglycerol-dependent serine/threonine kinase activity / Effects of PIP2 hydrolysis / Schmidt-Lanterman incisure / cellular response to chemical stress / regulation of insulin secretion involved in cellular response to glucose stimulus / membrane organization / positive regulation of endothelial cell apoptotic process / cell-cell junction organization / macrophage activation involved in immune response / regulation of release of sequestered calcium ion into cytosol / cellular response to ethanol / tight junction / synaptic transmission, GABAergic / response to morphine / signaling receptor activator activity / establishment or maintenance of epithelial cell apical/basal polarity / positive regulation of fibroblast migration / protein targeting to membrane / insulin secretion / positive regulation of cell-substrate adhesion / intermediate filament cytoskeleton / positive regulation of mucus secretion / positive regulation of wound healing / intercellular bridge / positive regulation of actin filament polymerization / Fc-gamma receptor signaling pathway involved in phagocytosis / positive regulation of Notch signaling pathway / cell-substrate adhesion / positive regulation of epithelial cell migration / cell leading edge / regulation of postsynaptic membrane neurotransmitter receptor levels / positive regulation of cytokinesis / locomotory exploration behavior / brush border / actin monomer binding / bicellular tight junction / Role of phospholipids in phagocytosis / regulation of peptidyl-tyrosine phosphorylation / vesicle-mediated transport / positive regulation of glial cell proliferation / lipopolysaccharide-mediated signaling pathway / enzyme activator activity / negative regulation of protein ubiquitination / 14-3-3 protein binding / cytoskeleton organization / p75NTR recruits signalling complexes / SHC1 events in ERBB2 signaling / response to interleukin-1 / secretion / establishment of localization in cell / cell periphery / positive regulation of synaptic transmission, GABAergic / positive regulation of glucose import / positive regulation of protein localization to plasma membrane / actin filament organization / Schaffer collateral - CA1 synapse / positive regulation of insulin secretion / phospholipid binding / Pre-NOTCH Transcription and Translation / positive regulation of neuron projection development / G alpha (z) signalling events / cellular response to insulin stimulus / cellular response to prostaglandin E stimulus / microtubule cytoskeleton / KEAP1-NFE2L2 pathway / MAPK cascade / cell migration / positive regulation of NF-kappaB transcription factor activity / cellular response to hypoxia / peptidyl-serine phosphorylation / positive regulation of canonical NF-kappaB signal transduction / negative regulation of neuron apoptotic process / positive regulation of MAPK cascade / protein kinase activity / intracellular signal transduction / endosome / cell cycle / apical plasma membrane / cell division / Golgi membrane / protein phosphorylation / intracellular membrane-bounded organelle / protein serine kinase activity / protein serine/threonine kinase activity / glutamatergic synapse Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Soriano, E.V. / Purkiss, A.G. / McDonald, N.Q. | ||||||
![]() | ![]() Title: aPKC Inhibition by Par3 CR3 Flanking Regions Controls Substrate Access and Underpins Apical-Junctional Polarization. Authors: Soriano, E.V. / Ivanova, M.E. / Fletcher, G. / Riou, P. / Knowles, P.P. / Barnouin, K. / Purkiss, A. / Kostelecky, B. / Saiu, P. / Linch, M. / Elbediwy, A. / Kjr, S. / O'Reilly, N. / ...Authors: Soriano, E.V. / Ivanova, M.E. / Fletcher, G. / Riou, P. / Knowles, P.P. / Barnouin, K. / Purkiss, A. / Kostelecky, B. / Saiu, P. / Linch, M. / Elbediwy, A. / Kjr, S. / O'Reilly, N. / Snijders, A.P. / Parker, P.J. / Thompson, B.J. / McDonald, N.Q. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 276.4 KB | Display | ![]() |
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PDB format | ![]() | 222.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 26.7 KB | Display | |
Data in CIF | ![]() | 35 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5li1C ![]() 5li9C ![]() 3a8wS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein / Protein/peptide , 2 types, 4 molecules ABFG
#1: Protein | Mass: 40333.383 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Protein/peptide | Mass: 2065.476 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() |
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-Non-polymers , 5 types, 38 molecules ![](data/chem/img/ADP.gif)
![](data/chem/img/AF3.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/SCN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/AF3.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/SCN.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | ChemComp-AF3 / #5: Chemical | ChemComp-MN / #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.94 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 32% Peg 2000 MME, 0.08 M KSCN |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 21, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 3.25→67.28 Å / Num. obs: 12144 / % possible obs: 99.6 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.172 / Net I/σ(I): 6.3 |
Reflection shell | Resolution: 3.25→3.43 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.475 / Mean I/σ(I) obs: 2.5 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3a8w Resolution: 3.25→67.28 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.57
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.25→67.28 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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